fiber.angle: Experimental! Calculating the orientation of muscle fibers
In GoodFibes: Detection and Reconstruction of Muscle Fibers from diceCT Image Data

fiber.angle

R Documentation

Experimental! Calculating the orientation of muscle fibers

Description

Calculating the angle of individual muscle fibers. This function can only calculate fiber angles around a central axis (x, y or z) or in reference to a particular "view" (plane). Fiber data is centered around the other axes.

Will eventually include an option for a tendon image stack. Not yet complete

Usage

fiber.angle(fib.list, axis, centered = TRUE, reference = "axis")

Arguments

`fib.list`	A list of muscle fiber paths generated by good.fibes or from the various cleaning and processing function (must contain $fiber.points).
`axis`	The axis around which angles will be calculated as a deviation from. Default is 3 (z). This axis is treated as the "z" axis for "plane" options.
`centered`	Should the data be centered on the other two axes before calculation.
`reference`	Should the angles be calculated about an axis (specified by "axis") or in reference to a plane ("plane.xz" or "plane.yz", where z is the value of "axis").

Value

A vector of angles in degrees corresponding to each fiber in the original list

Note

NOT TOTALLY VERIFIED YET, USE WITH CAUTION

Author(s)

J. Arbour

References

Arbour, J. 2023. GoodFibes: an R package for the detection of muscle fibers from diceCT scans. Integrative Organismal Biology 5(1): obad030.

Katzke, J., Puchenkov, P., Stark, H., and Economo, E. 2022. A Roadmap to Reconstructing Muscle Architecture from CT Data. Integrative Organismal Biology 4(1): 1-16.

Sullivan, S., McGechie, F., Middleton, K., and Holliday, C. 3D Muscle Architecture of the Pectoral Muscles of European Starling (Sturnus vulgaris).Integrative Organismal Biology 1(1):1-18.

Examples



olddir<-getwd()

data(ant.final)
fangle<-fiber.angle(ant.final,3)
fangle

cols<-color.scale(fangle, "blue", "red")
muscle.plot.stl(ant.final, cols=cols, df = 1)

setwd(olddir)

GoodFibes documentation built on Nov. 5, 2025, 5:23 p.m.